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Nabil-Fareed Alikhan - Curriculum Vitae

I am a bioinformatician with 11 years experience. I am neither clinically qualified nor active.

Education and Employment

Bioinformatics Scientific Programmer Dec 2018 - Current

Quadram Institute Bioscience, Norwich, United Kingdom

Duties include:

  • COG UK Consortium National effort for tracking COVID19 (SARSCoV2) through genome sequencing - I contribute analysis and data curation.
  • Building better bioinformatics infrastructure, moving towards open web platforms and cloud computing - I co-develop and maintain our in-house platforms in the institute.
  • Population genetics and pathogenesis of enteric pathogens, including Salmonella and E. coli
  • The Public Health Alliance for Genomic Epidemiology (PHA4GE) - infrastructure working group, aiming to find consensus in how we deploy Bioinformatics for public health across the world.
  • GitHub: http://github.com/happykhan
  • Funded by Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1) until March 2023.

Senior Research Fellow in Pathogen Bioinformatics Sep 2016 – Dec 2018

Warwick Medical School, University of Warwick, United Kingdom

Duties included integrating genomes from ancient metagenomes into EnteroBase, and the sequencing and analysis of 10,000 modern S. enterica. On-going development of EnteroBase and other software.

Research Fellow in Genomics of Bacterial Pathogens Dec 2014 – Sep 2016

Warwick Medical School, University of Warwick, United Kingdom

Duties included co-development of EnteroBase (enterobase.warwick.ac.uk), a web-resource for 'big data' genomic analysis of Enteropathogens and adapting existing robotic genotyping to perform library preparations for high-throughput sequencing.

Doctor of Philosophy (Microbiology) 2010 – 2015

University of Queensland, Australia

Primary Supervisor: Scott Beatson

Thesis title: Escherichia coli virulence: a genomic approach

Research Associate Mar 2009 – Nov 2009

School of Chemistry and Molecular Biosciences, University of Queensland, Australia

Duties included system administration and technical support for Linux servers and MacOSX workstations within the Beatson Microbial Genomics group.

Bachelor of Science (Honours – 1st Class) (Microbiology) 2009

University of Queensland, Australia

Thesis title: Comparative genome analysis of Escherichia coli VR 50

Research Associate Nov 2008 – Jan 2009

School of Chemistry and Molecular Biosciences, University of Queensland, Australia

Duties included programming software pipelines for bioinformatics especially for parallelization on high performance computer clusters; and server administration for sharing bacterial genomics data.

Bachelor of Science (Biochemistry) & Bachelor of Information Technology 2004 - 2008

University of Queensland, Australia

Skills

Bioinformatics

  • De novo assembly and mapping of sequencing reads
  • Comparative genome analysis
  • Phylogenetic inference e.g. PhyML & RAxML
  • Statistics: Python's matplotlib/numpy/scipy libraries and R.
  • Linux & command-line environment

Software Development

  • Development of EnteroBase, a web-resource serving over 600,000 genome assemblies, providing genotyping, genome analysis and curated metadata for over 1,600 users in a range of major institutions.
  • Development of BRIG software for visualisation of whole genome comparisons.
  • Developing novel visualisation and large-scale analysis tools, e.g. GrapeTree
  • Pipelines for high performance parallel computing architectures

Programming Languages

  • Full Stack Developer: Python, Java, Bash & Perl, Relationship databases (SQL), Web-frameworks (Python-Flask), JavaScript, HTML & PHP